Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species.

ABSTRACT: The ability to detect and reconstruct plasmids from genome assemblies is crucial for studying the evolution and spread of antimicrobial resistance and virulence in bacteria. Though long-read sequencing technologies have made reconstructing plasmids easier, most (97%) of the bacterial genome assemblies in the public domain are generated from short-read data. Work to compare plasmid reconstruction tools has focused primarily on E. coli, leaving gaps in our understanding of how well these tools perform on other, less well-characterized, taxa. Using high quality assemblies as ground truth, we benchmarked 12 plasmid detection tools (which identify plasmid contigs in assemblies) and four plasmid reconstruction tools (which group contigs from the same plasmid together). We tested their abi

SUBMITTER: Teixeira M 

PROVIDER: S-EPMC12324311 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature